The Under Subway (Japanese: ダークライナーDark Liner) runs from the Under to the Shadow Pokémon Laboratory. It was once used by miners before Cipher revamped it to transport Shadow Pokémon. The only way to access it, is to go down the stairs from the News Station, or the Under Colosseum. Inside are rooms where winners of the Under Colosseum challenges may stay in order to receive a promised Shadow Pokémon from Venus. Past the hallways is a system of staircases, that travel down to the bottom to access The Under Subway. In order to protect the station, security has been tightened with Trainers, each possessing their own Shadow Pokémon, all of whom work for Lady Venus. The Subway can also be accessed easily in an elevator which passes the whole system of staircases.

The train that runs on it, the Shadow Liner, is filled with cages to transport Ein's living experiments from the lab and to the Under. Wes and Rui tried to enter the Shadow Pokémon Laboratory via the Under Subway, only to have their path destroyed by a couple of Ein's minions.

It is unclear where it was originally sent to, as the Shadow Pokémon Lab was in the middle of the desert, and there was nothing there before it.